cDNA microarray readers are an invaluable tool for analysis of gene expression and for gene discovery through analysis of the fluorescent patterns of probes hybridized to a library of cDNA targets immobilized on a microscope slide. The instrumenation is based on a scanning confocal microscope in which laser excited fluorescence is spatially filtered and detected using a photomultiplier. Evaluation 16,000 different gene fragments is possible on a single microscope slide. Identification of unwanted, background fluorescence signals with modifications to the optical filtration has resulted in a significant improvement to the signal to noise ratio. Thus, lower levels of gene expression can now be determined. This is a continuation of Intramural Research Project Z01-RR-10476-02 BEI.